Added short hidden section at beginning of cookbook snippet sections explaining how to run the snippets

tweaking pehaps a listing environment for codeblock.
Related to BhallaLab/moose#225 .

* Recovered quickstart section in html, added tutorials placeholder and implemented rudimentary integration between doxygen and sphinx (dependecy on breathe sphinx extension)

* removed recursion limit change

* Added section to quickstart, and fixed a few minor typos in the install page

* Updated installation documentation with new mac osx brew install procedure. Made new section for OSX for consistency of format.

* removed some breathe related stuff from conf.py

* fixed minor typo in wildcard.py

* Recovered rdesigneur tutorial. Modified file by adding extended contents, commented out incomplete sections. Modified rdesigneur snippets page title to 'more rdesigneur examples' instead of just 'Rdesigneur'

* Added autorun statement to Compartment_net.py.

removed pyrun1.py documentation as it is exactly the same as pyrun.py.

updated vec information in quickstart to reflect actual ouput.

* uploaded fixed compartment_net.py without all my comments

* ...

Added squid demo to tutorials. Removed squid demo from quickstart. Wrote a bit of theory and history about squid demo. removed redundant modules.rst file.

removed pyrun1.py documentation as it is exactly the same as pyrun.py.

updated vec information in quickstart to reflect actual ouput.

Recovered rdesigneur tutorial. Modified file by adding extended contents, commented out incomplete sections. Modified rdesigneur snippets page title to 'more rdesigneur examples' instead of just 'Rdesigneur'

enabled.
May be some other test to test the gui without lauching it?

better formatting at the top of readme.

Quick link to packages and documents.

since -X is not enabled.